Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/a4cbc73bd4642aed14123d90f0d507/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/6364050760c5582cbdad0b85841682/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr1_69091-70008.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/6364050760c5582cbdad0b85841682/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/a4cbc73bd4642aed14123d90f0d507/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
==> STAGING COMPLETE (9 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr1_69091-70008.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:18480982, elapsed 0.1s, est remaining 1.1s, peak mem 84MB, user 0.1s, sys 0.1s, output queue size 912
progress 10% @chr1:37794183, elapsed 0.1s, est remaining 1.1s, peak mem 96MB, user 0.1s, sys 0.2s, output queue size 3562
progress 15% @chr1:65596448, elapsed 0.2s, est remaining 1.0s, peak mem 109MB, user 0.1s, sys 0.3s, output queue size 6302
progress 20% @chr1:113838544, elapsed 0.2s, est remaining 1.0s, peak mem 118MB, user 0.2s, sys 0.4s, output queue size 9051
progress 25% @chr1:155247782, elapsed 0.3s, est remaining 0.9s, peak mem 127MB, user 0.2s, sys 0.6s, output queue size 11396
progress 30% @chr1:179102287, elapsed 0.3s, est remaining 0.8s, peak mem 136MB, user 0.2s, sys 0.8s, output queue size 13874
progress 35% @chr1:209789667, elapsed 0.4s, est remaining 0.7s, peak mem 150MB, user 0.3s, sys 0.9s, output queue size 16299
progress 40% @chr1:246907551, elapsed 0.4s, est remaining 0.6s, peak mem 157MB, user 0.3s, sys 1.1s, output queue size 18704
progress 45% @chr2:32593915, elapsed 0.4s, est remaining 0.5s, peak mem 166MB, user 0.3s, sys 1.3s, output queue size 20992
progress 50% @chr2:74457334, elapsed 0.5s, est remaining 0.5s, peak mem 180MB, user 0.4s, sys 1.4s, output queue size 1755
progress 55% @chr2:113499257, elapsed 0.5s, est remaining 0.4s, peak mem 186MB, user 0.4s, sys 1.7s, output queue size 4283
progress 60% @chr2:171006147, elapsed 0.6s, est remaining 0.4s, peak mem 202MB, user 0.5s, sys 1.8s, output queue size 6983
progress 65% @chr2:202814702, elapsed 0.6s, est remaining 0.3s, peak mem 211MB, user 0.5s, sys 2.0s, output queue size 9257
progress 70% @chr2:233772261, elapsed 0.7s, est remaining 0.3s, peak mem 220MB, user 0.5s, sys 2.2s, output queue size 11730
progress 75% @chr3:25624297, elapsed 0.7s, est remaining 0.2s, peak mem 229MB, user 0.6s, sys 2.4s, output queue size 13954
progress 80% @chr3:49806073, elapsed 0.7s, est remaining 0.2s, peak mem 243MB, user 0.6s, sys 2.5s, output queue size 16428
progress 85% @chr3:102470394, elapsed 0.9s, est remaining 0.2s, peak mem 250MB, user 0.7s, sys 2.7s, output queue size 19072
progress 90% @chr3:139935375, elapsed 0.9s, est remaining 0.1s, peak mem 262MB, user 0.7s, sys 2.9s, output queue size 21661
progress 95% @chr3:188239635, elapsed 1.0s, est remaining 0.1s, peak mem 273MB, user 0.8s, sys 3.0s, output queue size 24068
progress 100% @chr4:25158953, elapsed 1.0s, est remaining 0.0s, peak mem 280MB, user 0.8s, sys 3.1s, output queue size 26305
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692767
output file size: 22305
reads: 1001089
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.000 user 0.000 sys 0.015 real
advance: 51084 calls 0.000 user 0.002 sys 0.021 real
calc: 100735 calls 0.000 user 0.006 sys 0.015 real
done: 1 calls 0.000 user 0.000 sys 0.012 real
execute: 1 calls 0.000 user 0.002 sys 1.950 real
fetch: 100735 calls 0.000 user 0.002 sys 0.015 real
fetch_ref: 100735 calls 0.082 user 0.047 sys 0.349 real
idle: 39 calls 0.003 user 0.009 sys 23.649 real
init: 1 calls 0.038 user 0.002 sys 0.042 real
region: 100735 calls 0.000 user 0.000 sys 0.016 real
tracker: 100735 calls 0.029 user 0.003 sys 0.084 real
overall: 294440960 mem 1.292 user 4.550 sys 3.079 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory